Few choreographers are as elegantly and uncomfortably topical as Bill T. Jones of the Bill T. Jones/Arnie Zane Dance Company, and even fewer put themselves at greater artistic risk.

In 1990 he grappled with race issues in a large, complex work named “Uncle Tom’s Cabin/The Promised Land,” echoing Harriet Beecher Stowe’s best-selling book that put the slur “Uncle Tom” into American vernacular. In 1994 he tackled the subject of mortal illness in “Still/Here,” a work panned by Arlene Croce of The New Yorker, who never attended the show.

Now, with his new multimedia work in its West Coast premiere at Yerba Buena Center for the Arts in San Francisco through Sunday, he has created what may be his most ambitious and complex piece to date, a fractured, uneven 80-minute movement drama entitled, “Fondly Do we Hope&. Fervently Do We Pray,” a phrase borrowed from Abraham Lincoln’s 1865 speech to the people of the United States near the close of the Civil War.

“Fondly” began as a search into the complexities of the character of Abraham Lincoln, including his ambivalence about race and slavery. Jones wanted to know: Was Lincoln a good man?

To create the work took two years, and in the piece that emerged, commissioned by the Ravinia Festival in Chicago where it premiered last month, Lincoln becomes the prism through which the American people are refracted. But the driving question shifts from Lincoln to the question, How do the rest of us measure up to the man? The answer? Not all that well.

That “Fondly” is no traditional story with a standard narrative form is evident long before the lights dim — text is broadcast into the theater before the dance gets underway, as though ghosts had already taken up residence.

The opening vignette plunges us into a story that is also in progress: the beautiful, fluid Shayla-Vie Jenkins dances a ruptured solo on a circular apron as the voice of an unseen boy names the parts of the face then works down the body. With a jolt we discover at the pelvis that it is a man’s body being itemized, possibly a slave body, or a body lusted after. In retrospect, the mover seems haunted but too late to be truly troubled.

Characters of different eras and cultures arise and multiple voices layer the air with various stories and multiple interpretations of such concepts as freedom of movement, states’ rights, and the autocracy of the individual.

Images of 1865 and 2009 are meant to slip together, but like a transmission that’s not in sync, the images never quite wholly or resonantly line up. As eloquently as he delivers his words, a tails-bedecked emcee, Jamyl Dobson — invoking a black Lincoln — has a script that is neither concrete enough nor sufficiently poetic to conjure up doubled spaces and simultaneous and distinct times.

The discrete parts of “Fondly” are often glorious, especially the buoyant solos on the apron, the exquisite ensemble work and the tormented duets. The music, delivered by musicians in the pit, slides across genres with sometimes heartbreaking agility. The main décor element, an ingenious giant magic lantern created from white diaphanous curtains, becomes a screen on which enormous silhouettes are projected and inside of which the “crowd” of dancers often gathers as though inside history.

But as a dive into the psyche of a divided nation, “Fondly” misses its mark by both holding too tightly to Lincoln yet not holding tightly enough. Meanwhile, the reputed heir to Lincoln’s legacy, President Barack Obama, is never overtly mentioned, an omission that seems driven by fear of history’s parallels more than fear of literalism. That result? “Fondly” is a daring but still unfinished work.